This study aimed to investigate bacterial diversity in Al-Asfar Lake, Al Ahsa Oasis, Saudi Arabia, based on a polyphasic approach. Water samples were collected and divided into two parts. For the culture-dependent approach, different media such as Tryptic Soy Agar (TSA), and Blood Agar (BA) were used. The obtained 29 isolates were diverse with respect to phenotypic characteristics revealed by VITEK. 18 isolates were selected for 16S rRNA sequencing based on the initial screening by VITEK. Since some types of bacteria do not grow on media, the DNA in the second part was isolated directly and subjected to metagenomic analysis. VITEK disclosed a total of 19 species belonging to 3 phyla: Pseudomonadota, Actinomycetota, and Bacillota, while the 16S rRNA sequencing revealed 12 species that could be amplified and sequenced. Metagenomic analysis exhibited variation in the relative abundance of 13 phyla, 18 classes, 20 families, 16 genera, and 24 species. Four dominant phyla are represented, including Firmicutes, Cyanobacteria, Bacteroidota, and Proteobacteria, respectively. Furthermore, functional gene screening revealed 33 functional categories including the metabolism of cofactors, vitamins, and xenobiotic biodegradation. This study affords insights into the bacterial diversity and fundamental biogeochemical processes in the lake and paves the way for the potential exploitation of microbial wealth in biotechnological applications.